[Samtools-help] Picard release 1.45

[Alec W. <al...@br...>]

Picard release 1.45
9 May 2011

- changes to avoid NPE when calling equals() method on SAMRecord

- New program CollectCDnaMetrics -- beta release

- Simplified CollectAlignmentSummaryMetrics.java and added 
PF_ALIGNED_BASES, and PF_MISMATCH_RATE to AlignedSummaryMetrics, 
CollectAlignmentSummaryMetrics.

- BAMRemoteFileTest.java: Move location of HTTP-accessed BAM from 
SourceForge web to Broad web, because SF doesn't serve this file 
reliably (perhaps because BAM is GZIP-encoded?)

- CollectAlignmentSummaryMetrics.java, MeanQualityByCycle.java, 
QualityScoreDistribution.java: Ignore non-primary alignments when 
gathering metrics.

- Refactored AbstractTextFileParser, TabbedTextFileParser, and 
BasicTextFileParser as AbstractInputParser, TabbedInputParser, and 
BasicInputParser.  All now have additional constructors that take 
InputStreams, and the old constructors that take Files are still there.  
Except for the name change, they should continue to work the same as before.

- ExtractIlluminaBarcodes.java: Fixed Option for BASECALLS_DIR

- CollectAlignmentSummaryMetrics.java: Fixed PF_HQ_ERROR_RATE, overflow 
error due to previous simplification of CollectAlignmentSummaryMetrics.java

- RevertSam.java: Do not copy non-primary alignments into reverted SAM.

- CommandLineProgram.java: Added an output of the elapsed time when a 
program ends.

- Changes to ensure that cleanup() is called on all instances of 
SortingCollection and SortingLongCollection after use, to ensure that 
temporary files are cleaned up ASAP.

- SeekableHTTPStream.java: Allow FTP as well as HTTP URL connection 
(patch courtesy of Lance Frohman).

-Alec